KABUL (Reuters) - The Afghan government on Sunday accused the Taliban of carrying out human rights abuses during two weeks of fighting for control of the northern city of Kunduz this month, even though insurgents say they sought to protect civilians.

Members of a family who fled Kunduz sit in a hotel room in Kabul, Afghanistan, October 12, 2015. REUTERS/Omar Sobhani

Though the Taliban only controlled the city for three days, fighting between the militants and Afghan security forces continued for two weeks, driving tens of thousands of residents to seek safety in neighboring provinces.

At least 50 civilians were killed and more than 350 wounded, according to hospital records compiled by the Afghanistan Independent Human Rights Commission (AIHRC), though it says the death toll is likely to be much higher.

Some 100,000 residents fled the clashes, according to U.N. estimates.

“Our people recounted examples of the atrocities committed by (the Taliban),” said Afghanistan’s Chief Executive Abdullah Abdullah at a press conference in the capital Kabul on Sunday. “It shows no change in the behavior and politics of this criminal group.”

AIHRC is calling for the government to investigate what it called “widespread and grave human rights violations” by militants during the battle for Kunduz.

Civilians were dragged out of their homes and killed in the street, used as human shields, and taken hostage by the insurgents, said a report released by the commission on Thursday.

The report also said evidence suggested women had been sexually assaulted by anti-government armed fighters during the offensive, echoing earlier reports by rights group Amnesty International that female health workers and prisoners had been raped during the siege.

A Taliban spokesman rejected the commission’s allegations.

“Eliminating enemy personnel and structures is part of war, however utmost care was taken in dealing with civilians and unwarranted trouble given to no one,” Taliban spokesman Zabihullah Mujahid said in a statement on Friday.

In addition, at least 22 patients and staff were killed in a U.S. air strike of a hospital run by Medecins Sans Frontieres on October 3.

Taliban fighters said they went into Kunduz under orders from their leader Mullah Akhtar Mohammad Mansour to win “hearts and minds.”

But many Kunduz residents who fled the fighting offered a very different version of events.

At a hotel in Kabul last week, where dozens of women and their children were staying after escaping Kunduz city without their husbands, several women said they had heard rumors that armed fighters were sexually assaulting women in the city.

“This was one of the main reasons I wanted to get my daughters out,” said Nadra Nahrinwal, who fled to Kabul in a car with her five daughters and son.